PDB Short entry for 1HAW HEADER OXIDOREDUCTASE 09-APR-01 1HAW TITLE X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN TITLE 2 COPPER FREE FORM AT 1.9 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NIR; COMPND 5 EC: 1.7.99.3, 1.7.2.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES XYLOSOXYDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 STRAIN: XYLOSOXIDANS; SOURCE 5 CELLULAR_LOCATION: PERIPLASM KEYWDS REDUCTASE, COPPER, BLUE COPPER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.ELLIS,F.E.DODD,R.W.STRANGE,M.PRUDENCIO,R.R.SAWERSEADY,S.S.HASNAIN REVDAT 4 13-DEC-23 1HAW 1 REMARK LINK REVDAT 3 09-MAY-12 1HAW 1 HEADER COMPND KEYWDS REMARK REVDAT 3 2 1 VERSN DBREF FORMUL REVDAT 2 24-FEB-09 1HAW 1 VERSN REVDAT 1 02-AUG-01 1HAW 0 JRNL AUTH M.J.ELLIS,F.E.DODD,R.W.STRANGE,M.PRUDENCIO,G.SAWERS, JRNL AUTH 2 R.R.EADY,S.S.HASNAIN JRNL TITL X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH JRNL TITL 2 PH AND IN COPPER-FREE FORM AT 1.9 A RESOLUTION JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 1110 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11468394 JRNL DOI 10.1107/S0907444901008654 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 28145 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1488 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2575 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.320 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.011 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.029 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.030 ; 0.050 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.173 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.238 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.119 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 4.700 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 13.100; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 28.000; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.306 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.987 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.619 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.487 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES WITH ZERO OCCUPANCY, NOT SEEN REMARK 3 IN THE DENSITY MAPS REMARK 4 REMARK 4 1HAW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-01. REMARK 100 THE DEPOSITION ID IS D_1290006077. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : TORROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29659 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 52.705 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.33100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1NDT MONOMER REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED USING THE WEISSENBERG METHOD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4K, 0.1M MAGNESIUM CHLORIDE, REMARK 280 0.1M TRIS-HCL PH8.5, PH 8.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.82350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.82350 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.82350 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 53.05300 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 91.89049 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 106.10600 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLN A 1 REMARK 475 ASP A 2 REMARK 475 ALA A 3 REMARK 475 ASP A 4 REMARK 475 LYS A 5 REMARK 475 PRO A 335 REMARK 475 ARG A 336 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 10 CG CD CE NZ REMARK 480 LYS A 27 CG CD CE NZ REMARK 480 SER A 28 OG REMARK 480 ASP A 48 CB CG OD1 OD2 REMARK 480 LYS A 49 CG CD CE NZ REMARK 480 GLN A 160 CG CD OE1 NE2 REMARK 480 LYS A 162 CG CD CE NZ REMARK 480 ARG A 168 CD NE CZ NH1 NH2 REMARK 480 LYS A 186 CG CD CE NZ REMARK 480 GLN A 202 CG CD OE1 NE2 REMARK 480 LYS A 217 CD CE NZ REMARK 480 LYS A 230 CG CD CE NZ REMARK 480 LYS A 315 CG CD CE NZ REMARK 480 GLU A 317 CD OE1 OE2 REMARK 480 LYS A 319 CG CD CE NZ REMARK 480 LYS A 326 CE NZ REMARK 480 LYS A 329 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ILE A 334 N PRO A 335 1.35 REMARK 500 NE2 HIS A 300 O HOH A 2136 2.03 REMARK 500 OE1 GLN A 18 NH2 ARG A 168 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2042 O HOH A 2136 3665 1.92 REMARK 500 NE2 HIS A 94 O HOH A 2136 3665 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 2 CB ASP A 2 CG -0.595 REMARK 500 ASP A 4 CB ASP A 4 CG -0.224 REMARK 500 GLN A 160 CD GLN A 160 NE2 -0.696 REMARK 500 ARG A 168 CG ARG A 168 CD 0.431 REMARK 500 LYS A 217 CG LYS A 217 CD 0.282 REMARK 500 ALA A 224 CA ALA A 224 CB 0.520 REMARK 500 LYS A 319 CB LYS A 319 CG -0.228 REMARK 500 LYS A 326 CD LYS A 326 CE 0.361 REMARK 500 ILE A 334 C PRO A 335 N -0.445 REMARK 500 PRO A 335 C ARG A 336 N -0.246 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 2 CB - CG - OD1 ANGL. DEV. = 14.2 DEGREES REMARK 500 ASP A 2 CB - CG - OD2 ANGL. DEV. = -12.8 DEGREES REMARK 500 ASP A 4 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 LYS A 5 O - C - N ANGL. DEV. = -11.4 DEGREES REMARK 500 MET A 44 CA - CB - CG ANGL. DEV. = 18.1 DEGREES REMARK 500 ASP A 48 CB - CA - C ANGL. DEV. = -19.6 DEGREES REMARK 500 ASP A 92 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 153 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 153 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 GLN A 160 CG - CD - NE2 ANGL. DEV. = -40.6 DEGREES REMARK 500 ASP A 176 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 LYS A 217 CB - CG - CD ANGL. DEV. = -20.4 DEGREES REMARK 500 ALA A 224 CB - CA - C ANGL. DEV. = -27.9 DEGREES REMARK 500 ALA A 224 N - CA - CB ANGL. DEV. = 33.9 DEGREES REMARK 500 ARG A 244 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 HIS A 300 CE1 - NE2 - CD2 ANGL. DEV. = 8.4 DEGREES REMARK 500 LYS A 326 CG - CD - CE ANGL. DEV. = -22.7 DEGREES REMARK 500 ILE A 334 CA - C - N ANGL. DEV. = 38.8 DEGREES REMARK 500 ILE A 334 O - C - N ANGL. DEV. = -44.3 DEGREES REMARK 500 PRO A 335 C - N - CA ANGL. DEV. = 27.3 DEGREES REMARK 500 PRO A 335 C - N - CD ANGL. DEV. = -28.6 DEGREES REMARK 500 PRO A 335 CA - C - N ANGL. DEV. = 13.3 DEGREES REMARK 500 PRO A 335 O - C - N ANGL. DEV. = -14.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 24 -78.77 -79.18 REMARK 500 ALA A 131 64.90 -153.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN A 160 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE A 334 -35.87 REMARK 500 PRO A 335 -13.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU1 A 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 CYS A 130 SG 122.4 REMARK 620 3 HIS A 139 ND1 98.2 120.1 REMARK 620 4 MET A 144 SD 87.2 109.0 115.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU1 A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HAU RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND REMARK 900 IN COPPER FREE FORM AT 1.9A RESOLUTION REMARK 900 RELATED ID: 1NDR RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM REMARK 900 ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1NDS RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF A SUBSTRATE BOUND BLUE COPPER NITRITE REMARK 900 REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1NDT RELATED DB: PDB REMARK 900 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS DBREF 1HAW A 1 336 UNP O68601 O68601_ALCXX 25 360 SEQRES 1 A 336 GLN ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR LEU SEQRES 2 A 336 VAL ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA THR SEQRES 3 A 336 LYS SER GLY PRO LYS VAL VAL GLU PHE THR MET THR ILE SEQRES 4 A 336 GLU GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR THR SEQRES 5 A 336 LEU GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 A 336 THR LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU THR SEQRES 7 A 336 LEU VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN VAL SEQRES 8 A 336 ASP PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA LYS SEQRES 9 A 336 LEU THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU ARG SEQRES 10 A 336 PHE LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS CYS SEQRES 11 A 336 ALA PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER GLY SEQRES 12 A 336 MET SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY LEU SEQRES 13 A 336 LYS ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG ALA SEQRES 14 A 336 TYR THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS GLY SEQRES 15 A 336 PRO ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA GLU SEQRES 16 A 336 SER TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU THR SEQRES 17 A 336 PRO SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA LEU SEQRES 18 A 336 THR GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU THR SEQRES 19 A 336 VAL LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR ARG SEQRES 20 A 336 PRO HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP GLU SEQRES 21 A 336 THR GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU GLU SEQRES 22 A 336 THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA LEU SEQRES 23 A 336 TYR THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU ASN SEQRES 24 A 336 HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA GLY SEQRES 25 A 336 HIS ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET SEQRES 26 A 336 LYS GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG HET CU1 A 501 1 HETNAM CU1 COPPER (I) ION FORMUL 2 CU1 CU 1+ FORMUL 3 HOH *149(H2 O) HELIX 1 1 ASP A 2 LEU A 6 5 5 HELIX 2 2 GLY A 98 THR A 106 5 9 HELIX 3 3 MET A 135 SER A 142 1 8 HELIX 4 4 THR A 192 ARG A 205 1 14 HELIX 5 5 THR A 222 ALA A 226 5 5 HELIX 6 6 ASN A 301 GLU A 307 1 7 SHEET 1 AA 4 HIS A 8 LYS A 10 0 SHEET 2 AA 4 VAL A 32 VAL A 45 1 O VAL A 32 N THR A 9 SHEET 3 AA 4 TYR A 74 ASN A 81 1 O TYR A 74 N VAL A 33 SHEET 4 AA 4 GLU A 112 LYS A 119 -1 O GLU A 112 N ASN A 81 SHEET 1 AB 3 HIS A 8 LYS A 10 0 SHEET 2 AB 3 VAL A 32 VAL A 45 1 O VAL A 32 N THR A 9 SHEET 3 AB 3 THR A 52 PHE A 58 -1 O LEU A 53 N MET A 44 SHEET 1 AC 4 LEU A 67 HIS A 70 0 SHEET 2 AC 4 SER A 145 LEU A 151 1 O THR A 147 N LEU A 67 SHEET 3 AC 4 GLY A 124 HIS A 129 -1 O GLY A 124 N VAL A 150 SHEET 4 AC 4 ASP A 92 PHE A 93 -1 O ASP A 92 N HIS A 129 SHEET 1 AD 6 HIS A 211 PHE A 214 0 SHEET 2 AD 6 ARG A 168 LEU A 177 -1 O PHE A 175 N VAL A 213 SHEET 3 AD 6 THR A 234 GLN A 241 1 O LEU A 236 N TYR A 170 SHEET 4 AD 6 SER A 281 THR A 288 -1 O SER A 281 N GLN A 241 SHEET 5 AD 6 GLY A 255 TRP A 259 -1 N ASP A 256 O LEU A 286 SHEET 6 AD 6 GLN A 269 LEU A 272 -1 O GLN A 269 N VAL A 258 SHEET 1 AE 2 LYS A 181 GLY A 182 0 SHEET 2 AE 2 LYS A 186 TYR A 187 -1 O LYS A 186 N GLY A 182 SHEET 1 AF 4 LEU A 227 LYS A 230 0 SHEET 2 AF 4 ALA A 311 GLU A 317 1 O HIS A 313 N LEU A 227 SHEET 3 AF 4 GLY A 293 ASN A 299 -1 O GLY A 293 N VAL A 316 SHEET 4 AF 4 PRO A 248 ILE A 251 -1 O HIS A 249 N LEU A 298 LINK ND1 HIS A 89 CU CU1 A 501 1555 1555 2.03 LINK SG CYS A 130 CU CU1 A 501 1555 1555 2.10 LINK ND1 HIS A 139 CU CU1 A 501 1555 1555 2.04 LINK SD MET A 144 CU CU1 A 501 1555 1555 2.59 CISPEP 1 PRO A 16 PRO A 17 0 5.34 CISPEP 2 MET A 62 PRO A 63 0 -6.63 SITE 1 AC1 4 HIS A 89 CYS A 130 HIS A 139 MET A 144 CRYST1 106.106 106.106 63.647 90.00 90.00 120.00 P 63 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009424 0.005441 0.000000 0.00000 SCALE2 0.000000 0.010882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015712 0.00000